Phage-induced disturbance of a marine sponge microbiome DOI Creative Commons
Leon X. Steiner, Lara Schmittmann,

Tanja Rahn

et al.

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: Nov. 26, 2024

Abstract Background Bacteriophages are known modulators of community composition and activity in environmental host-associated microbiomes. However, the impact single phages have on bacterial dynamics under viral predation, extent duration their effect, not completely understood. In this study, we combine morphological genomic characterization a novel marine phage, isolated from Baltic sponge Halichondria panicea , report first attempts controlled phage-manipulation natural sponge-associated Results We used culture-based culture-independent (16S rRNA gene amplicon sequencing) methods to investigate microbiomes with without addition phages. Upon application Maribacter specialist phage Panino conditions, were able detect community-wide shifts microbiome load after 72 h. While became more dissimilar over time presence phages, species evenness richness maintained. exposure, observed loss several low-abundance constituent taxa resident microbiota, while other originally underrepresented increased. Virulent likely induce disturbances, evident changes total microbial profile by specific elimination taxa, which leads an increase abundance opportunistic such as genera Vibrio Pseudoalteromonas Photobacterium . Conclusions Our findings suggest that diversity and, extension, its resilience depend maintenance members, irrespective abundance. Phage-induced disturbances can significantly alter structure promoting growth bacteria like shifting dysbiotic state. These insights highlight role bacteriophages shaping underscore potential for managing environments.

Language: Английский

Viral Communities Contribute More to the Lysis of Antibiotic-Resistant Bacteria than the Transduction of Antibiotic Resistance Genes in Anaerobic Digestion Revealed by Metagenomics DOI Creative Commons
Junya Zhang, Tiedong Lu, Yunpeng Song

et al.

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: 58(5), P. 2346 - 2359

Published: Jan. 24, 2024

Ecological role of the viral community on fate antibiotic resistance genes (ARGs) (reduction vs proliferation) remains unclear in anaerobic digestion (AD). Metagenomics revealed a dominance Siphoviridae and Podoviridae among 13,895 identified operational taxonomic units (vOTUs) within AD, only 21 vOTUs carried ARGs, which accounted for 0.57 ± 0.43% AD resistome. Conversely, ARGs locating plasmids integrative conjugative elements above 61.0%, indicating substantial potential conjugation driving horizontal gene transfer AD. Virus–host prediction based CRISPR spacer, tRNA, homology matches indicated that most viruses (80.2%) could not infect across genera. Among 480 high-quality metagenome assembly genomes, 95 were considered as putative antibiotic-resistant bacteria (pARB). Furthermore, lytic phages 66 pARBs devoid virus/host abundance ratios with an average value 71.7 extensive activity lysis. The infectivity phage was also elucidated through laboratory experiments concerning changes phage-to-host ratio, pH, temperature. Although metagenomic evidence dissemination by transduction found, higher proportion infecting suggested played greater reducing ARB numbers than spreading

Language: Английский

Citations

22
Methane-derived carbon flows into host–virus networks at different trophic levels in soil DOI Open Access
Sungeun Lee, Ella T. Sieradzki, Alexa M. Nicolas

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(32)

Published: Aug. 4, 2021

Significance The impact of soil viruses on prokaryotic hosts and their functional processes is largely unknown. While metagenomic sequencing microbial communities enables identification linkages between hosts, this does not necessarily identify contemporary interactions. To enable a detailed analysis active virus–host interactions individual populations, we focused the critical biogeochemical process methane (CH 4 ) oxidation followed transfer carbon from to associated in situ. Analysis 13 C-enriched DNA demonstrated that CH -derived transferred into viral biomass via both primary secondary utilizers suggests predation an important mechanism for releasing organic matrix.

Language: Английский

Citations

62
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes DOI Creative Commons
Rong Xia, Mingming Sun, José Luís Balcázar

et al.

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(7), P. 1004 - 1014

Published: April 17, 2023

The earthworm gut virome influences the structure and function of microbiome, which in turn worm health ecological functions. However, despite its soil quality implications, it remains elusive how intestinal phages respond to different environmental stress, such as pollution. Here we used metagenomics metatranscriptomics investigate interactions between their bacteria under benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg-1) stress stimulated microbial metabolism (1.74-fold control), enhanced antiphage defense system (n = 75) against infection (8 phage-host pairs). exposure resulted highest proportion lysogenic (88%), prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level (200 disrupted suppressed systems 29), leading increase phage-bacterium association (37 pairs) conversion lytic (lysogenic ratio declined 43%). Despite fluctuating interactions, phage-encoded AMGs related antioxidant pollutant degradation were enriched, apparently alleviate pollution stress. Overall, these findings expand our knowledge complex pollution-stressed guts, deepen understanding evolutionary roles phages.

Language: Английский

Citations

35
Phage Therapy in Germany—Update 2023 DOI Creative Commons
Christian Willy, Joachim J. Bugert, Annika Y. Claßen

et al.

Viruses, Journal Year: 2023, Volume and Issue: 15(2), P. 588 - 588

Published: Feb. 20, 2023

Bacteriophage therapy holds promise in addressing the antibiotic-resistance crisis, globally and Germany. Here, we provide an overview of current situation (2023) applied phage supporting research The authors, interdisciplinary group working on patient-focused bacteriophage research, addressed production, banks, susceptibility testing, clinical application, ongoing translational regulatory situation, network structure They identified critical shortcomings including lack trials, a paucity appropriate regulation shortage phages for use. Phage is currently being to limited number patients as individual treatment trials. There presently only one site Germany large-scale good-manufacturing-practice (GMP) clinic carrying out permission-free production medicinal products. Several banks exist, but due varying institutional policies, exchange among them limited. projects has remarkably increased recent years, some which are part structured networks. demand expansion capacities with defined quality standards, registry all treated clear therapeutic guidelines. Furthermore, medical field still poorly informed about therapy. status non-approval, however, may also be regarded advantageous, insufficiently restricted use without adequate scientific evidence effectiveness safety must prevented. In close coordination authorities, it seems sensible first allow centers treat following Belgian model. urgent need targeted networking funding, particularly help advance application phages.

Language: Английский

Citations

24
Symbiont transmission in marine sponges: reproduction, development, and metamorphosis DOI Creative Commons
Tyler J. Carrier, Manuel Maldonado, Lara Schmittmann

et al.

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: May 6, 2022

Abstract Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are in this early-diverging lineage. We describe vertical transmission is widespread but not universal, microbes vertically during a select window, properties of the microbiome depends on whether species high or low abundance sponge. Reproduction, development, symbiosis thus deeply rooted, why these partnerships remains central elusive tenet symbioses.

Language: Английский

Citations

38
Lytic archaeal viruses infect abundant primary producers in Earth’s crust DOI Creative Commons
Janina Rahlff, Victoria Turzynski, Sarah P. Esser

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: July 30, 2021

Abstract The continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use combination metagenomics virus-targeted direct-geneFISH (virusFISH) to show highly abundant carbon-fixing organisms the uncultivated genus Candidatus Altiarchaeum are frequent targets previously unrecognized in deep subsurface. Analysis CRISPR spacer matches display resistances Ca . Altiarchaea against eight predicted viral clades, which genomic relatedness across continents but similarity identified viruses. Based on metagenomic information, tag image putatively genome rich protospacers using fluorescence microscopy. VirusFISH reveals lytic lifestyle respective virus challenges previous predictions lysogeny prevails as dominant development over time imaging 18 samples from one ecosystem suggest sophisticated interplay diversification adapting CRISPR-mediated Altiarchaeum. We conclude infections primary producers with followed by cell lysis potentially jump-start heterotrophic carbon cycling these ecosystems.

Language: Английский

Citations

39
How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts DOI
Ramya Ganesan, Jürgen C. Wierz, Martin Kaltenpoth

et al.

Microbiology and Molecular Biology Reviews, Journal Year: 2022, Volume and Issue: 86(4)

Published: Oct. 27, 2022

Beneficial associations with bacteria are widespread across animals, spanning a range of symbiont localizations, transmission routes, and functions. While some these have evolved into obligate relationships permanent localization within the host, majority require colonization every host generation from environment or via maternal provisions.

Language: Английский

Citations

22
Glyphosate and spinetoram alter viral communities with different effects on antibiotic resistance genes in the bumblebee gut DOI
Qihe Tang, Yazhou Zhao,

Xi-Jie Li

et al.

Journal of Environmental Management, Journal Year: 2025, Volume and Issue: 374, P. 124079 - 124079

Published: Jan. 10, 2025

Language: Английский

Citations

0
Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process DOI
Zhengyuan Zhou, Songfeng Liu, Muhammad Saleem

et al.

Bioresource Technology, Journal Year: 2025, Volume and Issue: 419, P. 132081 - 132081

Published: Jan. 17, 2025

Language: Английский

Citations

0
Response of Soil Phage Communities and Prokaryote–Phage Interactions to Long-Term Drought DOI
Cong Liu, Zhijie Chen, Xinlei Wang

et al.

Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Soil moisture is a fundamental factor affecting terrestrial ecosystem functions. In this study, microscopic enumeration and joint metaviromic metagenomic sequencing were employed together to investigate the impact of prolonged drought on soil phage communities their interactions with prokaryotes in subtropical evergreen forest. Our findings revealed marked reduction abundances prokaryotic viral-like particles, by 73.1% 75.2%, respectively, significantly altered structure under drought. Meanwhile, substantially increased fraction containing lysogenic phages 163%, as well proportion temperate phages. Nonetheless, likely amplified negative prokaryote-phage given nearly doubled links co-occurrence network, higher frequency diversity antiphage defense systems found genomes. Under drought, exerted greater top-down control typical k-strategists including Acidobacteria Chloroflexi. Moreover, phage-encoded auxiliary metabolic genes may host metabolism biosynthesis-related Collectively, study underscore profound interactions. These results also emphasize importance managing levels during amendment microbiome manipulation account for influence

Language: Английский

Citations

0